NPASS Compound

Natural Product: NPC293629

Natural Product ID	NPC293629
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	(2S)-2-(3,4-Dimethoxyphenyl)-5-Hydroxy-7-[(2S,3R,4S,5S,6R)-3,4,5-Trihydroxy-6-[[(2R,3R,4R,5R,6S)-3,4,5-Trihydroxy-6-Methyloxan-2-Yl]Oxymethyl]Oxan-2-Yl]Oxy-2,3-Dihydrochromen-4-One
IUPAC Name	(2S)-2-(3,4-dimethoxyphenyl)-5-hydroxy-7-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-[[(2R,3R,4R,5R,6S)-3,4,5-trihydroxy-6-methyloxan-2-yl]oxymethyl]oxan-2-yl]oxy-2,3-dihydrochromen-4-one
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL3184988
PubChem CID	5284419
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid O-glycosides [CHEMONTID:0003533] Flavonoid-7-O-glycosides

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

Chemical Representations

RDKit 3D 80 84 0 0 0 0 0 0 0 0999 V2000 -8.1584 -1.1696 -2.3343 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.9714 0.3392 -2.2825 C 0 0 1 0 0 0 0 0 0 0 0 0 -8.7768 0.9059 -1.1558 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.8454 1.6882 -0.2544 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.7270 0.7430 0.1622 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.0415 0.1652 -1.0527 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.6730 0.4074 -1.0406 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.0029 -0.7884 -1.0265 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4969 -0.6150 -1.0164 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.8477 -1.9391 -1.2474 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6593 -2.7775 -0.0286 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6882 -1.9040 1.2061 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.0409 -0.5661 0.7971 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.6922 0.1950 1.8779 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5870 0.6483 2.1422 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7934 1.4297 3.2986 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0277 1.9065 3.6150 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1062 1.6300 2.8017 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4492 2.1276 3.1108 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5827 2.9948 4.0089 O 0 0 0 0 0 0 0 0 0 0 0 0 5.5748 1.5626 2.3286 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1338 1.5168 0.8743 C 0 0 1 0 0 0 0 0 0 0 0 0 6.2422 1.0980 -0.0143 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8695 1.9730 -0.8744 C 0 0 0 0 0 0 0 0 0 0 0 0 7.9137 1.5761 -1.7063 C 0 0 0 0 0 0 0 0 0 0 0 0 8.3539 0.2689 -1.6880 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7356 -0.6182 -0.8323 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6878 -0.2056 -0.0021 C 0 0 0 0 0 0 0 0 0 0 0 0 8.1876 -1.9281 -0.8229 O 0 0 0 0 0 0 0 0 0 0 0 0 7.6566 -2.9340 -0.0068 C 0 0 0 0 0 0 0 0 0 0 0 0 9.4030 -0.1818 -2.5063 O 0 0 0 0 0 0 0 0 0 0 0 0 10.0675 0.6802 -3.3965 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0544 0.5903 0.8342 O 0 0 0 0 0 0 0 0 0 0 0 0 2.9659 0.8706 1.6571 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6905 0.3964 1.3588 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2455 2.6765 4.7491 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.0506 0.0878 0.0701 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9933 -2.4851 2.2640 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5508 -3.8463 0.0575 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.6729 -1.7553 -1.9820 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.6292 0.6365 -2.2334 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.3026 -0.2914 0.8860 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.5527 2.0380 0.8849 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.7584 1.7354 -1.6435 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.2769 -1.6800 -2.7953 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.3190 -1.6087 -1.3374 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.0598 -1.4185 -2.9384 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.3808 0.7325 -3.2425 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.2500 0.1270 -0.5218 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.3973 2.5493 -0.7621 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9607 1.2330 0.7794 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1953 -0.9285 -1.0545 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3018 -1.4747 -0.2078 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2910 -1.3283 -1.9736 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2718 0.0167 -1.9272 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5326 -2.5166 -1.9356 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6097 -3.1896 -0.0775 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7057 -1.7061 1.5656 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2078 -0.8013 0.1446 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0791 1.6239 3.9106 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6996 0.4867 2.6403 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5096 2.1418 2.4595 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7315 2.5053 0.6217 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5426 3.0075 -0.9089 H 0 0 0 0 0 0 0 0 0 0 0 0 8.3844 2.2822 -2.3678 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2288 -0.9257 0.6528 H 0 0 0 0 0 0 0 0 0 0 0 0 8.4775 -3.6714 0.1711 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8253 -3.4888 -0.4617 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3944 -2.5593 1.0160 H 0 0 0 0 0 0 0 0 0 0 0 0 10.2408 1.6831 -2.9692 H 0 0 0 0 0 0 0 0 0 0 0 0 9.3825 0.8234 -4.2655 H 0 0 0 0 0 0 0 0 0 0 0 0 11.0213 0.2341 -3.6802 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5991 -0.1977 0.4583 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4518 2.8756 5.3598 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5169 -1.8110 2.8226 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3269 -3.5763 0.6140 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4729 -2.6445 -2.3978 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0130 -0.2787 1.8396 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.5887 3.0105 1.0372 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.9278 1.5905 -2.6159 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 2 0 16 17 1 0 17 18 2 0 18 19 1 0 19 20 2 0 19 21 1 0 21 22 1 0 22 23 1 0 23 24 2 0 24 25 1 0 25 26 2 0 26 27 1 0 27 28 2 0 27 29 1 0 29 30 1 0 26 31 1 0 31 32 1 0 22 33 1 0 33 34 1 0 34 35 2 0 17 36 1 0 13 37 1 0 12 38 1 0 11 39 1 0 10 40 1 0 6 41 1 0 5 42 1 0 4 43 1 0 3 44 1 0 41 2 1 0 37 9 1 0 35 15 1 0 34 18 1 0 28 23 1 0 1 45 1 0 1 46 1 0 1 47 1 0 2 48 1 6 3 49 1 1 4 50 1 6 5 51 1 1 6 52 1 1 8 53 1 0 8 54 1 0 9 55 1 6 10 56 1 6 11 57 1 6 12 58 1 1 13 59 1 6 16 60 1 0 21 61 1 0 21 62 1 0 22 63 1 6 24 64 1 0 25 65 1 0 28 66 1 0 30 67 1 0 30 68 1 0 30 69 1 0 32 70 1 0 32 71 1 0 32 72 1 0 35 73 1 0 36 74 1 0 38 75 1 0 39 76 1 0 40 77 1 0 42 78 1 0 43 79 1 0 44 80 1 0 M END

Standard InCHIKey	GUMSHIGGVOJLBP-SLRPQMTOSA-N
Standard InCHI	InChI=1S/C29H36O15/c1-11-22(32)24(34)26(36)28(41-11)40-10-20-23(33)25(35)27(37)29(44-20)42-13-7-14(30)21-15(31)9-17(43-19(21)8-13)12-4-5-16(38-2)18(6-12)39-3/h4-8,11,17,20,22-30,32-37H,9-10H2,1-3H3/t11-,17-,20+,22-,23+,24+,25-,26+,27+,28+,29+/m0/s1
SMILES	C[C@H]1[C@@H]([C@H]([C@H]([C@H](OC[C@@H]2[C@H]([C@@H]([C@H]([C@H](Oc3cc(c4C(=O)C[C@@H](c5ccc(c(c5)OC)OC)Oc4c3)O)O2)O)O)O)O1)O)O)O

Calculated Properties

Physi-Chem Properties

MedChem Properties

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

ADMET: Distribution

ADMET: Metabolism

ADMET: Excretion

ADMET: Toxicity

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO3477	Plantago asiatica	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[2488968]
NPO3477	Plantago asiatica	Species	Plantaginaceae	Eukaryota	n.a.	seed	n.a.	PMID[2610694]
NPO8918	Plantago depressa	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26562611]
NPO3477	Plantago asiatica	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO8918	Plantago depressa	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO3477	Plantago asiatica	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8918	Plantago depressa	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO8918	Plantago depressa	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3477	Plantago asiatica	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3477	Plantago asiatica	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO8918	Plantago depressa	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO3477	Plantago asiatica	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO8918	Plantago depressa	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO8918	Plantago depressa	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3477	Plantago asiatica	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

NP Quantity Composition/Concentration

Organism ID	Organism Name	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

Biological Activity

Activity Type	# Activity
Potency	8

Activity Type	# Activity
Others	8

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT2	Others	Unspecified	n.a.	Potency	n.a.	21786.8	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	n.a.	Potency	n.a.	66212.6	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	n.a.	Potency	n.a.	59012.1	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	n.a.	Potency	n.a.	5949.5	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	n.a.	Potency	n.a.	68310.7	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	n.a.	Potency	n.a.	53024.9	nM	PubChem BioAssay data set
NPT2	Others	Unspecified	n.a.	Potency	n.a.	46875	nM	PubChem BioAssay data set

In vivo activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

Experimental ADME

Experiment Model	Experiment Tissue	ADME Type	ADME Relation	ADME Value	ADME Unit	Reference

Experimental Toxicity

Quantitative toxicity

Experiment Model	Experiment Organism	Toxicity Type	Toxicity Relation	Toxicity Value	Toxicity Unit	Reference
-	Rattus norvegicus	NOAEL	=	8000.0	mg/kg-day	ToxVal

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity	Carcinogenicity	Mutagenicity	Cardiotoxicity	Respiratory Toxicity	Eye Irritation	Endocrine Disruption

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]

Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

● The left chart: Distribution of similarity level between NPC293629 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	14454
0.1-0.2	29975
0.2-0.3	4604
0.3-0.4	702
0.4-0.5	97
0.5-0.6	20
0.6-0.7	2
0.7-0.8	0
0.8-0.85	3
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8415	Intermediate Similarity	NPC44328
0.8415	Intermediate Similarity	NPC79056
0.8049	Intermediate Similarity	NPC271270
0.7857	Intermediate Similarity	NPC43587
0.631	Remote Similarity	NPC219163
0.6196	Remote Similarity	NPC97285
0.5955	Remote Similarity	NPC236934
0.5926	Remote Similarity	NPC469622
0.5833	Remote Similarity	NPC105095
0.5833	Remote Similarity	NPC177731
0.5833	Remote Similarity	NPC725
0.5816	Remote Similarity	NPC67134
0.5789	Remote Similarity	NPC241016
0.5714	Remote Similarity	NPC479450
0.5632	Remote Similarity	NPC97052
0.5568	Remote Similarity	NPC39351
0.5567	Remote Similarity	NPC190450
0.5521	Remote Similarity	NPC142860
0.5521	Remote Similarity	NPC152538
0.5521	Remote Similarity	NPC246469
0.5521	Remote Similarity	NPC89088
0.5444	Remote Similarity	NPC29830
0.5408	Remote Similarity	NPC291124
0.5408	Remote Similarity	NPC131157
0.5165	Remote Similarity	NPC3293
0.5158	Remote Similarity	NPC472382

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC293629 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4132
0.1-0.2	4869
0.2-0.3	135
0.3-0.4	12
0.4-0.5	1
0.5-0.6	0
0.6-0.7	0
0.7-0.8	0
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8415	Intermediate Similarity	NPD7074	Phase 3

Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.
Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity

B: biological targets similarity

C: networks similarity

D: cell-based bioactivity similarity

E: similarity based on clinical data